The Glaucoma-Associated Olfactomedin Domain of Myocilin Forms Polymorphic Fibrils That Are Constrained by Partial Unfolding and Peptide Sequence

The glaucoma-associated olfactomedin domain of myocilin (myoc-OLF) is a recent addition to the growing list of disease-associated amyloidogenic proteins. Inherited, disease-causing myocilin variants aggregate intracellularly instead of being secreted to the trabecular meshwork, which is a scenario toxic to trabecular meshwork cells and leads to early onset of ocular hypertension, the major risk factor for glaucoma. Here we systematically structurally and biophysically dissected myoc-OLF to better understand its amyloidogenesis. Under mildly destabilizing conditions, wild-type myoc-OLF adopts non-native structures that readily fibrillize when incubated at a temperature just below the transition for tertiary unfolding. With buffers at physiological pH, two main endpoint fibril morphologies are observed: (a) straight fibrils common to many amyloids and (b) unique micron-length, ~ 300 nm or larger diameter, species that lasso oligomers, which also exhibit classical spectroscopic amyloid signatures. Three disease-causing variants investigated herein exhibit non-native tertiary structures under physiological conditions, leading to a variety of growth rates and a fibril morphologies. In particular, the well-documented D380A variant, which lacks calcium, forms large circular fibrils. Two amyloid-forming peptide stretches have been identified, one for each of the main fibril morphologies observed. Our study places myoc-OLF within the larger landscape of the amylome and provides insight into the diversity of myoc-OLF aggregation that plays a role in glaucoma pathogenesis.     

Parallel Explicit and Implicit Control of Reaching

Background

Human movement can be guided automatically (implicit control) or attentively (explicit control). Explicit control may be engaged when learning a new movement, while implicit control enables simultaneous execution of multiple actions. Explicit and implicit control can often be assigned arbitrarily: we can simultaneously drive a car and tune the radio, seamlessly allocating implicit or explicit control to either action. This flexibility suggests that sensorimotor signals, including those that encode spatially overlapping perception and behavior, can be accurately segregated to explicit and implicit control processes.

Methodology/Principal Findings

We tested human subjects'' ability to segregate sensorimotor signals to parallel control processes by requiring dual (explicit and implicit) control of the same reaching movement and testing for interference between these processes. Healthy control subjects were able to engage dual explicit and implicit motor control without degradation of performance compared to explicit or implicit control alone. We then asked whether segregation of explicit and implicit motor control can be selectively disrupted by studying dual-control performance in subjects with no clinically manifest neurologic deficits in the presymptomatic stage of Huntington''s disease (HD). These subjects performed successfully under either explicit or implicit control alone, but were impaired in the dual-control condition.

Conclusion/Significance

The human nervous system can exert dual control on a single action, and is therefore able to accurately segregate sensorimotor signals to explicit and implicit control. The impairment observed in the presymptomatic stage of HD points to a possible crucial contribution of the striatum to the segregation of sensorimotor signals to multiple control processes.     

Implicit and Explicit Illusory Correlation as a Function of Political Ideology

Research has demonstrated that people who embrace different ideological orientations often show differences at the level of basic cognitive processes. For instance, conservatives (vs. liberals) display an automatic selective attention for negative (vs. positive) stimuli, and tend to more easily form illusory correlations between negative information and minority groups. In the present work, we further explored this latter effect by examining whether it only involves the formation of explicit attitudes or it extends to implicit attitudes. To this end, following the typical illusory correlation paradigm, participants were presented with members of two numerically different groups (majority and minority) each performing either a positive or negative behaviour. Negative behaviors were relatively infrequent, and the proportion of positive and negative behaviors within each group was the same. Next, explicit and implicit (i.e., IAT-measured) attitudes were assessed. Results showed that conservatives (vs. liberals) displayed stronger explicit as well as implicit illusory correlations effects, forming more negative attitudes toward the minority (vs. majority) group at both the explicit and implicit level.     

Phosphono Peptide Nucleic Acids with a Constrained Hydroxyproline-Based Backbone

Abstract

DNA mimics representing negatively charged analogues of peptide nucleic acids (PNAs), particularly hetero-oligomers constructed from alternating phosphono-PNA residues (pPNA) and monomers on the base of trans-4-hydroxy-L-proline (HypNA) as well as mimics composed of phosphono-HypNA monomers (pHypNA) were tested in a set of in vitro and in vivo assays, and they demonstrated a high potential for the use in nucleic acid based diagnostic, isolation of nucleic acids and antisense experiments.     

Sequential Unfolding of Beta Helical Protein by Single-Molecule Atomic Force Microscopy

The parallel βhelix is a common fold among extracellular proteins, however its mechanical properties remain unexplored. In Gram-negative bacteria, extracellular proteins of diverse functions of the large ‘TpsA’ family all fold into long βhelices. Here, single-molecule atomic force microscopy and steered molecular dynamics simulations were combined to investigate the mechanical properties of a prototypic TpsA protein, FHA, the major adhesin of Bordetella pertussis. Strong extension forces were required to fully unfold this highly repetitive protein, and unfolding occurred along a stepwise, hierarchical process. Our analyses showed that the extremities of the βhelix unfold early, while central regions of the helix are more resistant to mechanical unfolding. In particular, a mechanically resistant subdomain conserved among TpsA proteins and critical for secretion was identified. This nucleus harbors structural elements packed against the βhelix that might contribute to stabilizing the N-terminal region of FHA. Hierarchical unfolding of the βhelix in response to a mechanical stress may maintain β-helical portions that can serve as templates for regaining the native structure after stress. The mechanical properties uncovered here might apply to many proteins with β-helical or related folds, both in prokaryotes and in eukaryotes, and play key roles in their structural integrity and functions.     

Molecular Modelling of Six-Ring Agarose Chains: Effects of Explicit and Implicit Solvent

A study on the molecular dynamics of agarose-type oligosaccharide chains in water is presented. In the field of molecular modelling one is able to use either explicit water molecules or a representative bulk dielectric constant: the two methods are compared here. The starting conformation was taken from X-ray fibre diffraction data for agarose double helices, which are neutral molecules. The resulting trajectories were analysed for the behaviour of dihedral linkages, and these were compared to systematic searches performed on isolated agarobiose and neo-agarobiose units. The results showed that when explicit water molecules are used the oligosaccharide chains are stiffer and have a reduced mobility.Electronic Supplementary Material available.     

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular generalized Born (GB) implicit-solvent model, as implemented in the AMBER package. We systematically investigate small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size. The speedups in conformational sampling for GB relative to PME simulations, are highly system- and problem-dependent. Where the simulation temperatures for PME and GB are the same, the corresponding speedups are approximately onefold (small conformational changes), between ∼1- and ∼100-fold (large changes), and approximately sevenfold (mixed case). The effects of temperature on speedup and free-energy landscapes, which may differ substantially between the solvent models, are discussed in detail for the case of miniprotein folding. In addition to speeding up conformational sampling, due to algorithmic differences, the implicit solvent model can be computationally faster for small systems or slower for large systems, depending on the number of solute and solvent atoms. For the conformational changes considered here, the combined speedups are approximately twofold, ∼1- to 60-fold, and ∼50-fold, respectively, in the low solvent viscosity regime afforded by the implicit solvent. For all the systems studied, 1) conformational sampling speedup increases as Langevin collision frequency (effective viscosity) decreases; and 2) conformational sampling speedup is mainly due to reduction in solvent viscosity rather than possible differences in free-energy landscapes between the solvent models.     

Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution

The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system’s electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions. The simulations are performed by employing the open-boundary molecular dynamics method that allows for simulation of open systems that can exchange mass and linear momentum with the environment. In our open-boundary molecular dynamics approach, the computational burden is drastically alleviated by embedding the DNA molecule in a mixed explicit/implicit salt-bathing solution. In the explicit domain, the water molecules and ions are both overtly present in the system, whereas in the implicit water domain, only the ions are explicitly present and the water is described as a continuous dielectric medium. Water molecules are inserted and deleted into/from the system in the intermediate buffer domain that acts as a water reservoir to the explicit domain, with both water molecules and ions free to enter or leave the explicit domain. Our approach is general and allows for efficient molecular simulations of biomolecules solvated in bathing salt solutions at any ionic strength condition.     

Implicit and Explicit Representations of Hand Position in Tool Use

Understanding the interactions of visual and proprioceptive information in tool use is important as it is the basis for learning of the tool''s kinematic transformation and thus skilled performance. This study investigated how the CNS combines seen cursor positions and felt hand positions under a visuo-motor rotation paradigm. Young and older adult participants performed aiming movements on a digitizer while looking at rotated visual feedback on a monitor. After each movement, they judged either the proprioceptively sensed hand direction or the visually sensed cursor direction. We identified asymmetric mutual biases with a strong visual dominance. Furthermore, we found a number of differences between explicit and implicit judgments of hand directions. The explicit judgments had considerably larger variability than the implicit judgments. The bias toward the cursor direction for the explicit judgments was about twice as strong as for the implicit judgments. The individual biases of explicit and implicit judgments were uncorrelated. Biases of these judgments exhibited opposite sequential effects. Moreover, age-related changes were also different between these judgments. The judgment variability was decreased and the bias toward the cursor direction was increased with increasing age only for the explicit judgments. These results indicate distinct explicit and implicit neural representations of hand direction, similar to the notion of distinct visual systems.     

Sodium Perchlorate Effects on the Helical Stability of a Mainly Alanine Peptide

Sodium perchlorate salt (NaClO₄) is commonly used as an internal intensity standard in ultraviolet resonance Raman (UVRR) spectroscopy experiments. It is well known that NaClO₄ can have profound effects on peptide stability. The impact of NaClO₄ on protein stability in UVRR experiments has not yet been fully investigated. It is well known from experiment that protein stability is strongly affected by the solution composition (water, salts, osmolytes, etc.). Therefore, it is of the utmost importance to understand the physical basis on which the presence of salts and osmolytes in the solution impact protein structure and stability. The aim of this study is to investigate the effects of NaClO₄, on the helical stability of an alanine peptide in water. Based upon replica-exchange molecular dynamics data, it was found that NaClO₄ solution strongly stabilizes the helical state and that the number of pure helical conformations found at room temperature is greater than in pure water. A thorough investigation of the anion effects on the first and second solvation shells of the peptide, along with the Kirkwood-Buff theory for solutions, allows us to explain the physical mechanisms involved in the observed specific ion effects. A direct mechanism was found in which ClO₄⁻ ions are strongly attracted to the folded backbone.     

Implicit and Explicit Contributions to Object Recognition: Evidence from Rapid Perceptual Learning

The present study investigated implicit and explicit recognition processes of rapidly perceptually learned objects by means of steady-state visual evoked potentials (SSVEP). Participants were initially exposed to object pictures within an incidental learning task (living/non-living categorization). Subsequently, degraded versions of some of these learned pictures were presented together with degraded versions of unlearned pictures and participants had to judge, whether they recognized an object or not. During this test phase, stimuli were presented at 15 Hz eliciting an SSVEP at the same frequency. Source localizations of SSVEP effects revealed for implicit and explicit processes overlapping activations in orbito-frontal and temporal regions. Correlates of explicit object recognition were additionally found in the superior parietal lobe. These findings are discussed to reflect facilitation of object-specific processing areas within the temporal lobe by an orbito-frontal top-down signal as proposed by bi-directional accounts of object recognition.     

Conformational Analysis of a Synthetic Antimicrobial Peptide in Water and Membrane-Mimicking Solvents: A Molecular Dynamics Simulation Study

We have investigated structural and dynamic properties of the synthetic peptide hlF1-11 (GRRRSVQWCA, i.e., the first 11 N-terminal amino acids of the human lactoferrin protein) in water, 250 mM NaCl solution, 50% (V/V) water–trifluoroethanol mixture, and in the membrane mimetic 4:4:1 methanol–chloroform–water mixture. For comparison, we have also performed analogous simulations for the biologically inactive control peptide featuring Ala substitutions in the 2, 3, 6 and 9 positions of the hlF1-11 sequence. Statistical analyses of the trajectories indicate that only in the membrane-mimicking medium hlF1-11 adopts preferentially a conformation suitable to interact effectively with the membrane. In this conformation the peptide cationic region is rather flexible and elongated, while the C-terminal hydrophobic moiety appears as a more rigid hairpin-shaped loop approximately perpendicular to the cationic region. No such conformation is statistically relevant for the control peptide.     

Multidisciplinary Views on Applying Explicit and Implicit Motor Learning in Practice: An International Survey

Background

A variety of options and techniques for causing implicit and explicit motor learning have been described in the literature. The aim of the current paper was to provide clearer guidance for practitioners on how to apply motor learning in practice by exploring experts’ opinions and experiences, using the distinction between implicit and explicit motor learning as a conceptual departure point.

Methods

A survey was designed to collect and aggregate informed opinions and experiences from 40 international respondents who had demonstrable expertise related to motor learning in practice and/or research. The survey was administered through an online survey tool and addressed potential options and learning strategies for applying implicit and explicit motor learning. Responses were analysed in terms of consensus (≥ 70%) and trends (≥ 50%). A summary figure was developed to illustrate a taxonomy of the different learning strategies and options indicated by the experts in the survey.

Results

Answers of experts were widely distributed. No consensus was found regarding the application of implicit and explicit motor learning. Some trends were identified: Explicit motor learning can be promoted by using instructions and various types of feedback, but when promoting implicit motor learning, instructions and feedback should be restricted. Further, for implicit motor learning, an external focus of attention should be considered, as well as practicing the entire skill. Experts agreed on three factors that influence motor learning choices: the learner’s abilities, the type of task, and the stage of motor learning (94.5%; n = 34/36). Most experts agreed with the summary figure (64.7%; n = 22/34).

Conclusion

The results provide an overview of possible ways to cause implicit or explicit motor learning, signposting examples from practice and factors that influence day-to-day motor learning decisions.     

Tensile Mechanics of Alanine-Based Helical Polypeptide: Force Spectroscopy versus Computer Simulations

In nature, an α-helix is commonly used to build thermodynamically stable and mechanically rigid protein conformations. In view of growing interest in the mechanical rigidity of proteins, we measured the tensile profile of an alanine-based α-helical polypeptide on an atomic-force microscope to investigate the basic mechanics of helix extension with minimal interference from side-chain interactions. The peptide was extended to its maximum contour length with much less force than in reported cases of poly-L-Glu or poly-L-Lys, indicating that chain stiffness strongly depended on the physicochemical properties of side chains, such as their bulkiness. The low tensile-force extension originated presumably in locally unfolded parts because of spontaneous structural fluctuations. In 50% trifluoroethanol, the well-known helix-promoting agent, the rigidity of the sample polypeptide was markedly increased. Computer simulations of the peptide-stretching process showed that a majority of constituent residues underwent a transition from an α-helical to an extended conformation by overcoming an energy barrier around ψ ∼0° on the Ramachandran plot. The observed lability of an isolated helix signified the biological importance of the lateral bundling of helices to maintain a rigid protein structure.     

Large Scale Brain Functional Networks Support Sentence Comprehension: Evidence from Both Explicit and Implicit Language Tasks

Previous studies have indicated that sentences are comprehended via widespread brain regions in the fronto-temporo-parietal network in explicit language tasks (e.g., semantic congruency judgment tasks), and through restricted temporal or frontal regions in implicit language tasks (e.g., font size judgment tasks). This discrepancy has raised questions regarding a common network for sentence comprehension that acts regardless of task effect and whether different tasks modulate network properties. To this end, we constructed brain functional networks based on 27 subjects’ fMRI data that was collected while performing explicit and implicit language tasks. We found that network properties and network hubs corresponding to the implicit language task were similar to those associated with the explicit language task. We also found common hubs in occipital, temporal and frontal regions in both tasks. Compared with the implicit language task, the explicit language task resulted in greater global efficiency and increased integrated betweenness centrality of the left inferior frontal gyrus, which is a key region related to sentence comprehension. These results suggest that brain functional networks support both explicit and implicit sentence comprehension; in addition, these two types of language tasks may modulate the properties of brain functional networks.     

Structure-Activity Relationships of Conformationally Constrained Peptide Analogues of Loop 2 of Brain-Derived Neurotrophic Factor

Abstract: Brain-derived neurotrophic factor (BDNF) promotes the survival of various neuronal populations and thus shows potential in the treatment of neurodegenerative disease. However, BDNF is not pharmacokinetically optimal for use as a therapeutic agent. As a step toward the development of low-molecular-weight BDNF-like drugs, we have designed a series of small, conformationally constrained peptides of various sizes using the three-dimensional structure of BDNF derived by homology modeling as a template. When tested in cultures of embryonic chick sensory neurons the peptides produced concentration-dependent inhibition of BDNF-mediated neuronal survival and caused both a rightward shift and depression of the maximum of the BDNF concentration-response curve. The compounds had no effect on the survival response to nerve growth factor and were without intrinsic trophic or toxic effects when added to cultures alone. With the aid of pharmacodynamic simulations we demonstrated that the inhibitory activity of the active peptides is consistent with them acting as competitive antagonists of BDNF for its high-affinity receptor, trkB. An alanine scan of the largest peptide identified several residues important in mediating the inhibitory action of the peptides. We intend to use the data from these studies to develop small peptidic BDNF-like agonists.     

Implicit and Explicit Anti-Fat Bias among a Large Sample of Medical Doctors by BMI,Race/Ethnicity and Gender

Overweight patients report weight discrimination in health care settings and subsequent avoidance of routine preventive health care. The purpose of this study was to examine implicit and explicit attitudes about weight among a large group of medical doctors (MDs) to determine the pervasiveness of negative attitudes about weight among MDs. Test-takers voluntarily accessed a public Web site, known as Project Implicit®, and opted to complete the Weight Implicit Association Test (IAT) (N = 359,261). A sub-sample identified their highest level of education as MD (N = 2,284). Among the MDs, 55% were female, 78% reported their race as white, and 62% had a normal range BMI. This large sample of test-takers showed strong implicit anti-fat bias (Cohen’s d = 1.0). MDs, on average, also showed strong implicit anti-fat bias (Cohen’s d = 0.93). All test-takers and the MD sub-sample reported a strong preference for thin people rather than fat people or a strong explicit anti-fat bias. We conclude that strong implicit and explicit anti-fat bias is as pervasive among MDs as it is among the general public. An important area for future research is to investigate the association between providers’ implicit and explicit attitudes about weight, patient reports of weight discrimination in health care, and quality of care delivered to overweight patients.     

Solid Phase Synthesis of a Hydroxypyrrolidine Derivative and its Use in Solid Phase Peptide Synthesis as Constrained Statine Mimic

As part of our efforts to design constrained peptide mimics and introduce them in peptide sequences, we set up the synthesis of racemic N-Fmoc protected hydroxypyrrolidine by reduction of the corresponding oxopyrroline. Hydroxypyrrolidines are synthesized using amino acid building block and β-ketoester via a 4-steps solid supported route on Wang resin beads. The hydroxypyrrolidine template can be seen as a constrained mimic of statine. As proof of concept, the pseudopeptide JMV 2776, incorporating this new statine mimic has been synthesized. We replaced the phenyl statine building block in the sequence of known BACE 1/2 inhibitors by 5-benzyl 2-methyl 4-hydroxypyrrolidine, using conventional Fmoc SPPS on Rink amide PS resin. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Implicit Attitudes towards People with Intellectual Disabilities: Their Relationship with Explicit Attitudes,Social Distance,Emotions and Contact

Implicit attitude research has expanded rapidly over the last decade and is seen as very promising as it counters biases present in much attitude research such as social desirability. However, most research in the area of intellectual disabilities has focused on explicit attitudes alone. This study examined implicit attitudes to this population and also examined their association with emotional reactions and contact, which have previously been found to have a significant influence on attitudes and stigma. A web based survey consisting of a single target Implicit Association Test, measures of explicit attitudes, social distance, and emotional reactions towards and contact with individuals with intellectual disabilities was completed by 326 adult UK residents. Implicit attitudes were not significantly associated with explicit attitudes, social distance or emotional reactions. Instead there were small to moderate associations between emotional reactions and explicit attitudes and social distance. Implicit attitudes did not vary according to participants’ level of contact with individuals with intellectual disabilities, type of the contact relationship (voluntary versus involuntary), gender or educational attainment. In contrast, these participant characteristics did affect explicit attitudes and social distance. Implicit attitudes towards individuals with intellectual disabilities were somewhat negative and, unlike explicit attitudes and stigma, did not vary according to participant demographics or contact. As they may have a negative impact on the lives of people with intellectual disabilities, implicit attitudes merit increased attention in research and interventions in the intellectual disabilities field.     

Unfolding study of a trimeric membrane protein AcrB

The folding of a multi‐domain trimeric α‐helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two‐state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter‐subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate‐limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrB_Δloop, from the SDS unfolded state. The CD spectrum of the refolded AcrB_Δloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re‐association of the trimer might be the limiting factor to obtain folded wild‐type AcrB.